The finite element method using an unstructured tetrahedral mesh is one of the most effective methods for the 3-D modelling of marine magnetotelluric data that are strongly affected by bathymetry, because it enables us to incorporate both small-scale and regional-scale bathymetry into a computational mesh with a practical number of elements. The authors applied a 3-D inversion scheme using mesh of this type to marine magnetotelluric problems for the first time and verified its applicability. Forward calculations for two bathymetry models demonstrated that the results obtained with an unstructured tetrahedral mesh are close to the reference solutions. To evaluate the forward calculation results, we developed a general TM-mode analytical formulation for a 2-D sinusoidal topography. Moreover, synthetic inversion test results confirmed that a 3-D inversion scheme with an unstructured tetrahedral mesh enables us to recover subseafloor resistivity structure properly even for a model including a land-sea boundary as well as seafloor undulations. The verified inversion schemewas subsequently applied to a set ofmarinemagnetotelluric data observed around the Iheya North Knoll, themiddle Okinawa Trough. 3-Dmodelling using a mesh with precise bathymetry demonstrated that the data observed around the Iheya North Knoll are strongly affected by bathymetry, especially by the sea-depth differences between the depression of the trough and the shallow East China Sea. The estimated resistivity structure under the knoll is characterized by a conductive surface layer underlain by a resistive layer. The conductive layer implies permeable pelagic/hemipelagic sediments, which are consistent with a previous seismological study. Furthermore, the conductive layer has a resistive part immediately below the knoll, which is regarded as the consolidated magma intrusion that formed the knoll. Furthermore, at a depth of 10 km, we found that the resistor underneath the knoll extends to the southeast, implying that subseafloor resistivity under the Volcanic Arc Migration Phenomenon area is more resistive than the surroundings due to the presence of consolidated magma.